pdbe-molstar 3.5.0 → 3.7.0

package/lib/superposition-sifts-mapping.js

@@ -1,153 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.alignAndSuperposeWithSIFTSMapping = alignAndSuperposeWithSIFTSMapping;
-const int_1 = require("molstar/lib/mol-data/int");
-const minimize_rmsd_1 = require("molstar/lib/mol-math/linear-algebra/3d/minimize-rmsd");
-const element_1 = require("molstar/lib/mol-model/structure/structure/element");
-const sifts_mapping_1 = require("./sifts-mapping");
-function alignAndSuperposeWithSIFTSMapping(structures, options) {
-    var _a, _b;
-    const indexMap = new Map();
-    for (let i = 0; i < structures.length; i++) {
-        let includeResidueTest = (_a = options === null || options === void 0 ? void 0 : options.includeResidueTest) !== null && _a !== void 0 ? _a : _includeAllResidues;
-        if ((options === null || options === void 0 ? void 0 : options.applyTestIndex) && !options.applyTestIndex.includes(i))
-            includeResidueTest = _includeAllResidues;
-        buildIndex(structures[i], indexMap, i, (_b = options === null || options === void 0 ? void 0 : options.traceOnly) !== null && _b !== void 0 ? _b : true, includeResidueTest);
-    }
-    const index = Array.from(indexMap.values());
-    // TODO: support non-first structure pivots
-    const pairs = findPairs(structures.length, index);
-    const zeroOverlapPairs = [];
-    const failedPairs = [];
-    const entries = [];
-    for (const p of pairs) {
-        if (p.count === 0) {
-            zeroOverlapPairs.push([p.i, p.j]);
-        }
-        else {
-            const [a, b] = getPositionTables(index, p.i, p.j, p.count);
-            const transform = minimize_rmsd_1.MinimizeRmsd.compute({ a, b });
-            if (Number.isNaN(transform.rmsd)) {
-                failedPairs.push([p.i, p.j]);
-            }
-            else {
-                entries.push({ transform, pivot: p.i, other: p.j });
-            }
-        }
-    }
-    return { entries, zeroOverlapPairs, failedPairs };
-}
-function getPositionTables(index, pivot, other, N) {
-    const xs = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
-    const ys = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
-    let o = 0;
-    for (const { pivots } of index) {
-        const a = pivots[pivot];
-        const b = pivots[other];
-        if (!a || !b)
-            continue;
-        const l = Math.min(a[2] - a[1], b[2] - b[1]);
-        // TODO: check if residue types match?
-        for (let i = 0; i < l; i++) {
-            let eI = (a[1] + i);
-            xs.x[o] = a[0].conformation.x(eI);
-            xs.y[o] = a[0].conformation.y(eI);
-            xs.z[o] = a[0].conformation.z(eI);
-            eI = (b[1] + i);
-            ys.x[o] = b[0].conformation.x(eI);
-            ys.y[o] = b[0].conformation.y(eI);
-            ys.z[o] = b[0].conformation.z(eI);
-            o++;
-        }
-    }
-    return [xs, ys];
-}
-function findPairs(N, index) {
-    const pairwiseCounts = [];
-    for (let i = 0; i < N; i++) {
-        pairwiseCounts[i] = [];
-        for (let j = 0; j < N; j++)
-            pairwiseCounts[i][j] = 0;
-    }
-    for (const { pivots } of index) {
-        for (let i = 0; i < N; i++) {
-            if (!pivots[i])
-                continue;
-            const lI = pivots[i][2] - pivots[i][1];
-            for (let j = i + 1; j < N; j++) {
-                if (!pivots[j])
-                    continue;
-                const lJ = pivots[j][2] - pivots[j][1];
-                pairwiseCounts[i][j] = pairwiseCounts[i][j] + Math.min(lI, lJ);
-            }
-        }
-    }
-    const ret = [];
-    for (let j = 1; j < N; j++) {
-        ret[j - 1] = { i: 0, j, count: pairwiseCounts[0][j] };
-    }
-    // TODO: support non-first structure pivots
-    // for (let i = 0; i < N - 1; i++) {
-    //     let max = 0, maxJ = i;
-    //     for (let j = i + 1; j < N; j++) {
-    //         if (pairwiseCounts[i][j] > max) {
-    //             maxJ = j;
-    //             max = pairwiseCounts[i][j];
-    //         }
-    //     }
-    //     ret[i] = { i, j: maxJ, count: max };
-    // }
-    return ret;
-}
-function _includeAllResidues() { return true; }
-function buildIndex(structure, index, sI, traceOnly, includeTest) {
-    const loc = element_1.StructureElement.Location.create(structure);
-    for (const unit of structure.units) {
-        if (unit.kind !== 0 /* Unit.Kind.Atomic */)
-            continue;
-        const { elements, model } = unit;
-        loc.unit = unit;
-        const map = sifts_mapping_1.SIFTSMapping.Provider.get(model).value;
-        if (!map)
-            return;
-        const { dbName, accession, num } = map;
-        const chainsIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
-        const residuesIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
-        const traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex;
-        while (chainsIt.hasNext) {
-            const chainSegment = chainsIt.move();
-            residuesIt.setSegment(chainSegment);
-            while (residuesIt.hasNext) {
-                const residueSegment = residuesIt.move();
-                const rI = residueSegment.index;
-                if (!dbName[rI])
-                    continue;
-                const traceElement = traceElementIndex[rI];
-                let start, end;
-                if (traceOnly) {
-                    start = traceElement;
-                    if (start === -1)
-                        continue;
-                    end = start + 1;
-                }
-                else {
-                    start = elements[residueSegment.start];
-                    end = elements[residueSegment.end - 1] + 1;
-                }
-                loc.element = (traceElement >= 0 ? traceElement : start);
-                if (!includeTest(loc, rI, start, end))
-                    continue;
-                const key = `${dbName[rI]}-${accession[rI].split('-')[0]}-${num[rI]}`;
-                if (!index.has(key)) {
-                    index.set(key, { key, pivots: { [sI]: [unit, start, end] } });
-                }
-                else {
-                    const entry = index.get(key);
-                    if (!entry.pivots[sI]) {
-                        entry.pivots[sI] = [unit, start, end];
-                    }
-                }
-            }
-        }
-    }
-}